Acquisition of nonmaternal Enterobacteriaceae by infants delivered in hospitals

Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load

BACKGROUND

Infants are at a high risk of acquiring fatal infections, and their treatment relies on functioning antibiotics. Antibiotic resistance genes (ARGs) are present in high numbers in antibiotic-naive infants' gut microbiomes, and infant mortality caused by resistant infections is high. The role of antibiotics in shaping the infant resistome has been studied, but there is limited knowledge on other factors that affect the antibiotic resistance burden of the infant gut.

OBJECTIVES

Our objectives were to determine the impact of early exposure to formula on the ARG load in neonates and infants born either preterm or full term. Our hypotheses were that diet causes a selective pressure that influences the microbial community of the infant gut, and formula exposure would increase the abundance of taxa that carry ARGs.

METHODS

Cross-sectionally sampled gut metagenomes of 46 neonates were used to build a generalized linear model to determine the impact of diet on ARG loads in neonates. The model was cross-validated using neonate metagenomes gathered from public databases using our custom statistical pipeline for cross-validation.

RESULTS

Formula-fed neonates had higher relative abundances of opportunistic pathogens such as Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella pneumoniae, Klebsiella oxytoca, and Clostridioides difficile. The relative abundance of ARGs carried by gut bacteria was 69% higher in the formula-receiving group (fold change, 1.69; 95% CI: 1.12-2.55; P = 0.013; n = 180) compared to exclusively human milk-fed infants. The formula-fed infants also had significantly less typical infant bacteria, such as Bifidobacteria, that have potential health benefits.

CONCLUSIONS

The novel finding that formula exposure is correlated with a higher neonatal ARG burden lays the foundation that clinicians should consider feeding mode in addition to antibiotic use during the first months of life to minimize the proliferation of antibiotic-resistant gut bacteria in infants.

Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants

Colonization of the gastrointestinal tract with microorganisms during infancy represents a critical control point for shaping life-long immune-mediated disease susceptibility. Abnormal colonization or an imbalance of microbes, termed dysbiosis, is implicated in several diseases. Consequently, recent research has aimed at understanding ways to manipulate a dysbiotic microbiome during infancy to resemble a normal, healthy microbiome. However, one of the fundamental issues in microbiome research is characterizing what a "normal" infant microbiome is based on geography, ethnicity and cultural variations. This review provides a comprehensive account of what is currently known about the infant microbiome from a global context. In general, this review shows that the influence of cultural variations in feeding practices, delivery modes and hygiene are the biggest contributors to microbial variability. Despite geography or race, all humans have similar microbial succession during infancy.

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers’ breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.

The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) even in the absence of antibiotic exposure. Here, Pärnänen et al. analyse breast milk as well as infant and maternal gut microbiomes, and show that some of the infant gut ARGs are transferred from the mothers.

Bifidobacterial strains in the intestines of newborns originate from their mothers

The gastrointestinal tract is believed to be colonized rapidly with bacteria immediately from birth. The source of these intestinal microbes is an ongoing topic of interest because increasing evidence suggests that the composition of the initial intestinal bacterial colonization strongly affects health. In particular, the source of bifidobacteria has received marked attention because these bacteria are suggested to play a crucial role in protecting against susceptibility to diverse diseases later in life. However, the source of these microbes has remained unclear. Recently, it was confirmed that mothers transmit their unique bifidobacterial strains to their children shortly after birth. The transmitted strains predominate during early infancy, suggesting that maternal intestinal bifidobacteria are an important source of the infant gut microbiota. Accordingly, maintenance of a healthy, balanced gut microbiota during pregnancy has an important positive influence on the newborn gut microbiota.

The impact of early life gut colonization on metabolic and obesogenic outcomes: what have animal models shown us?

The rise in the occurrence of obesity to epidemic proportions has made it a global concern. Great difficulty has been experienced in efforts to control this growing problem with lifestyle interventions. Thus, attention has been directed to understanding the events of one of the most critical periods of development, perinatal life. Early life adversity driven by maternal obesity has been associated with an increased risk of metabolic disease and obesity in the offspring later in life. Although a mechanistic link explaining the relationship between maternal and offspring obesity is still under investigation, the gut microbiota has come forth as a new factor that may play a role modulating metabolic function of both the mother and the offspring. Emerging evidence suggests that the gut microbiota plays a much larger role in mediating the risk of developing non-communicable disease, including obesity and metabolic dysfunction in adulthood. With the observation that the early life colonization of the neonatal and postnatal gut is mediated by the perinatal environment, the number of studies investigating early life gut microbial establishment continues to grow. This paper will review early life gut colonization in experimental animal models, concentrating on the role of the early life environment in offspring gut colonization and the ability of the gut microbiota to dictate risk of disease later in life.

Gut microbiota in preterm infants with gross blood in stools: A prospective, controlled study

OBJECTIVE

Gross blood in stools is a peculiar entity in preterm infants, but little is known about its etiology. As gut microbiota can be distorted in preterm infants, we aimed to evaluate the gut microbiota in infants with gross blood in stools.

STUDY DESIGN

In a prospective, controlled, single-center study, we enrolled all infants born before 34 weeks of gestational age presenting gross blood in stools that was either completely isolated or associated with mild clinical symptoms or radiological signs. Each case was paired with two controls who were hospitalized in the same unit and were matched for gestational age and birth weight. The diversity of the gut microbiota was analyzed using 16S rRNA gene PCR and temporal temperature gel electrophoresis. We calculated a diversity score corresponding to the number of operational taxonomic units present in the microbiota.

RESULTS

Thirty-three preterm infants with gross blood in stools were matched with 57 controls. Clinical characteristics were similar in cases and controls. There was no statistically significant difference in the diversity score between the two groups, but microbiota composition differed. The proportion of infants with Escherichia coli was significantly higher in cases than in controls (p=0.045) and the opposite pattern occurred for Staphylococcus sp. (p=0.047).

CONCLUSION

Dysbiosis could be a risk factor for gross blood in stools in preterm infants. Additional, larger studies are needed to confirm the implications of the presence of different genotypes of E. coli and to evaluate preventive actions such as the prophylactic use of probiotics and/or prebiotics.

Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota

Objectives

Bifidobacterium species are one of the major components of the infant's intestine microbiota. Colonization with bifidobacteria in early infancy is suggested to be important for health in later life. However, information remains limited regarding the source of these microbes. Here, we investigated whether specific strains of bifidobacteria in the maternal intestinal flora are transmitted to their infant's intestine.

Materials and Methods

Fecal samples were collected from healthy 17 mother and infant pairs (Vaginal delivery: 12; Cesarean section delivery: 5). Mother's feces were collected twice before delivery. Infant's feces were collected at 0 (meconium), 3, 7, 30, 90 days after birth. Bifidobacteria isolated from feces were genotyped by multilocus sequencing typing, and the transitions of bifidobacteria counts in infant's feces were analyzed by quantitative real-time PCR.

Results

Stains belonging to Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium catenulatum, Bifidobacterium longum subsp. longum, and Bifidobacterium pseudocatenulatum, were identified to be monophyletic between mother's and infant's intestine. Eleven out of 12 vaginal delivered infants carried at least one monophyletic strain. The bifidobacterial counts of the species to which the monophyletic strains belong, increased predominantly in the infant's intestine within 3 days after birth. Among infants delivered by C-section, monophyletic strains were not observed. Moreover, the bifidobacterial counts were significantly lower than the vaginal delivered infants until 7 days of age.

Conclusions

Among infants born vaginally, several Bifidobacterium strains transmit from the mother and colonize the infant's intestine shortly after birth. Our data suggest that the mother's intestine is an important source for the vaginal delivered infant's intestinal microbiota.

Influence of maternal bifidobacteria on the development of gut bifidobacteria in infants

Intestinal microbiota plays an important role in human health by influencing metabolic activities that result in the creation of energy and absorbable nutrients, a barrier to the colonization of pathogens, and stimulation of the immune system. The development of fecal microbiota in neonates is crucial because those bacteria are the first to colonize the sterile intestine of the neonates and, thus, have a significant effect on the host. Initial colonization is also relevant to the final composition of the permanent microbiota in adults. Bifidobacteria are predominant in the fecal microbiota of infants, and, therefore, they are important to an understanding of how commensal bifidobacteria is established in the intestine of infants. While the mother's bifidobacteria are considered to significantly influence the infant's bifidobacteria, it is not clear whether a specific bifidobacterial strain transmits vertically from mother to infant and what factors of the mother before delivery influence the establishment of intestinal bifidobacteria in infants. This review focuses on the impact of maternal bifidobacteria on the development of gut bifidobacteria in the infant and suggests that there is cumulative evidence regarding bifidobacterial transfer from the maternal gut or breast milk to the infant gut.

Establishment of the bacterial fecal community during the first month of life in Brazilian newborns

OBJECTIVE

The establishment of the intestinal microbiota in newborns is a critical period with possible long-term consequences for human health. In this research, the development of the fecal microbiota of a group of exclusively breastfed neonates living in low socio-economic conditions in the city of São Paulo, Brazil, during the first month of life, was studied.

METHODS

Fecal samples were collected from ten neonates on the second, seventh, and 30(th) days after birth. One of the neonates underwent antibiotic therapy. Molecular techniques were used for analysis; DNA was extracted from the samples, and 16S rRNA libraries were sequenced and phylogenetically analyzed after construction. A real-time polymerase chain reaction (PCR) was performed on the samples taken from the 30(th) day to amplify DNA from Bifidobacterium sp.

RESULTS

The primary phylogenetic groups identified in the samples were Escherichia and Clostridium. Staphylococcus was identified at a low rate. Bifidobacterium sp. was detected in all of the samples collected on the 30(th) day. In the child who received antibiotics, a reduction in anaerobes and Escherichia, which was associated with an overgrowth of Klebsiella, was observed throughout the experimental period.

CONCLUSION

The observed pattern of Escherichia predominance and reduced Staphylococcus colonization is in contrast with the patterns observed in neonates living in developed countries.

Influence of maternal bifidobacteria on the establishment of bifidobacteria colonizing the gut in infants

The aim of this study was to examine the influence of maternal intestinal and vaginal bifidobacteria on the establishment of bifidobacteria colonizing the gut in infants. Fecal samples from 110 healthy pregnant mothers within 1 mo before delivery and their babies at 1 mo of age and 100 vaginal swabs from the mother within 7 d before delivery were collected at a maternity hospital in Fukuoka city, Japan. The fecal and vaginal samples were assayed by PCR to detect Bifidobacterium species and by real-time PCR assays to estimate the bifidobacterial number. The detection of Bifidobacterium breve in the mothers' feces was significantly associated with increases in both the bifidobacterial counts and number of Bifidobacterium species in the babies' feces. In addition, a cesarean section was significantly associated with both a decrease in the counts and diversity of bifidobacteria in the babies' feces. The number of Bifidobacterium species detected in the vaginal swabs of mothers were not associated with either the bifidobacterial counts or the diversity of bifidobacteria in the babies' feces. The most important determinants of intestinal bifidobacteria in infants were the colonization of B. breve in the mothers' gut and vaginal delivery.

Maternal breast-milk and intestinal bifidobacteria guide the compositional development of the Bifidobacterium microbiota in infants at risk of allergic disease

BACKGROUND

The sources and the impact of maternal bacteria on the initial inoculum of the intestinal microflora of newborn infants remain elusive.

OBJECTIVE

To assess the association between maternal breast-milk and fecal bifidobacteria and infants' fecal bifidobacteria.

METHODS

Sixty-one mother-infant pairs were included, special emphasis being placed on the maternal allergic status. Bifidobacteria were analysed by a direct PCR method in fecal samples from mothers at 30-35 weeks of gestation and from infants at 1 month of age and from breast-milk samples 1 month post-partum.

RESULTS

Fecal Bifidobacterium adolescentis and Bifidobacterium bifidum colonization frequencies and counts among mother-infant pairs correlated significantly (P=0.005 and 0.02 for frequencies, respectively, and P=0.002 and 0.01 for counts, respectively). Only infants of allergic, atopic mothers were colonized with B. adolescentis. Each of the breast-milk samples contained bifidobacteria [median 1.4 x 10(3) bacterial cells/mL; interquartile range (IQR) 48.7-3.8 x 10(3)]. Bifidobacterium longum was the most frequently detected species in breast-milk. Allergic mothers had significantly lower amounts of bifidobacteria in breast-milk compared with non-allergic mothers [median 1.3 x 10(3) bacterial cells/mL (IQR 22.4-3.0 x 10(3)) vs. 5.6 x 10(3) bacterial cells/mL (1.8 x 10(3)-1.8 x 10(4)), respectively, (P=0.004)], and their infants had concurrently lower counts of bifidobacteria in feces [3.9 x 10(8) bacterial cells/g (IQR 6.5 x 10(6)-1.5 x 10(9)) in infants of allergic mothers, vs. 2.5 x 10(9) bacterial cells/g (6.5 x 10(8)-3.2 x 10(10)) in infants of non-allergic mothers, P=0.013].

CONCLUSIONS

Breast-milk contains significant numbers of bifidobacteria and the maternal allergic status further deranges the counts of bifidobacteria in breast-milk. Maternal fecal and breast-milk bifidobacterial counts impacted on the infants' fecal Bifidobacterium levels. Breast-milk bacteria should thus be considered an important source of bacteria in the establishment of infantile intestinal microbiota.

Development of intestinal bifidobacteria and lactobacilli in breast-fed neonates

BACKGROUND & AIMS

Neonates are subject to numerous factors that affect normal intestinal colonization. This study was to quantify bifidobacteria and lactobacilli in the faeces of breast-fed neonates using quantitative real-time PCR assay, and to investigate the effects of different delivery on the development of bifidobacteria or lactobacilli.

METHODS

The faecal bifidobacteria and lactobacilli of 40 healthy breast-fed neonates were studied prospectively. Twenty infants were vaginally delivered (VD), and 20 by caesarean delivery (CD) with prophylactically 4 g intravenous cefradine administered to their mothers three times. The faecal bifidobacteria and lactobacilli of neonates were consecutively quantified by SYBR Green I-based real-time PCR assay in the first 7 days after birth.

RESULTS

The mean levels of bifidobacteria increased from 5.1 to 9.3 in the VD group vs from less than 4.6 to 8.7 in the CD group. The bifidobacteria colonization levels in six samples in the CD group were lower than the limit of detection on day 2. The mean levels of bifidobacteria in the VD group were significantly higher than in the CD group (p<0.05). The mean levels of lactobacilli increased from 4.9 to 7.2 in the VD group vs from 4.9 to 6.9 in the CD group. There was no statistical difference between two groups during the first week (p>0.05). The development of bifidobacteria and lactobacilli showed significant interindividual differences in all infants studied.

CONCLUSIONS

Primary intestinal bifidobacteria in neonates by caesarean may be disturbed more significantly than lactobacilli.

Intestinal microflora in early infancy: composition and development

The neonatal intestinal microbiota is a complex ecosystem composed of numerous genera, species and strains of bacteria. This enormous cell mass performs a variety of unique activities that affect both the colonic and systemic physiology. Its primary activities include nutritive, metabolic, immunological and protective functions. Most studies of infants have been based on faecal samples using the classical plating techniques with culturing on specific media. The limitations of these methods must be taken into account when evaluating the varying results of the different studies. The establishment of the gut microbial population is not strictly a succession in the ecological sense; it is rather a complex process influenced by microbial and host interactions and by external and internal factors. The climax intestinal flora is attained in successive stages. The foetal intestine is sterile and bathed in swallowed amniotic fluid. Following delivery, multiple different antigens challenge the intestine of the newborn. The maternal intestinal flora is a source of bacteria for the neonatal gut. The bacterial flora is usually heterogeneous during the first few days of life, independently of feeding habits. After the first week of life, a stable bacterial flora is usually established. In full-term infants a diet of breast milk induces the development of a flora rich in Bifidobacterium spp. Other obligate anaerobes, such as Clostridium spp. and Bacteroides spp., are more rarely isolated and also enterobacteria and enterococci are relatively few. During the corresponding period, formula-fed babies are often colonized by other anaerobes in addition to bifidobacteria and by facultatively anaerobic bacteria; the development of a "bifidus flora" is unusual. In other studies the presence of a consistent number of bifidobacteria in infants delivered in large urban hospitals has not been demonstrated, whether the babies were bottle fed or exclusively breastfed. The predominant faecal bacteria were coliforms and bacteroides. According to these studies, environmental factors may be more important than breastfeeding in gut colonization after delivery. Environmental factors are indeed extremely important for the intestinal colonization of infants born by caesarean section. In these infants, the establishment of a stable flora characterized by a low incidence of Bacteroides spp. and by the isolation of few other bacteria is consistently delayed. In extremely low-birthweight infants, hospitalization in neonatal intensive care units, characterized by prolonged antibiotic therapy, parenteral nutrition, delayed oral feedings and intubation seems to affect the composition of the intestinal microbiota. The gut is colonized by a small number of bacterial species; Lactobacillus and Bifidobacteria spp. are seldom, if ever, identified. According to the few studies so far performed, the predominant species are Enterococcus faecalis, E. coli, Enterobacter cloacae, Klebsiella pneumoniae, Staphylococcus epidermidis and Staphylococcus haemolyticus. Hygienic conditions and antimicrobial procedures strongly influence the intestinal colonization pattern.

Duodenal microflora in very-low-birth-weight neonates and relation to necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in the neonatal period. Small-bowel overgrowth with aerobic gram-negative bacteria has previously been implicated in the development of NEC. This prospective study performed quantitative bacteriology on 422 duodenal aspirates collected from 122 very-low-birth-weight (<1,500-g) newborns, at the time of routine changing of nasogastric tubes. Isolates of Enterobacteriaceae were typed by repetitive extragenic, palindromic PCR and pulsed-field gel electrophoresis. One or more samples from 50% of these infants yielded gram-negative bacteria, predominantly Escherichia coli, Klebsiella spp., and Enterobacter spp., with counts up to 10(8) CFU/g. The proportion of samples with gram-negative bacteria increased with postnatal age, while the percentage of sterile samples declined. Molecular typing revealed marked temporal clustering of indistinguishable strains. All infants had been fed prior to isolation of gram-negative organisms. Antibiotic use had no obvious effect on colonization with Enterobacteriaceae. There were 15 episodes of suspected NEC (stage I) and 8 confirmed cases of NEC (2 stage II and 6 stage III) during the study period. Duodenal aspirates were collected prior to clinical onset in 13 episodes of NEC. Seven of these yielded Enterobacteriaceae, of which five strains were also isolated from infants without NEC. Very-low-birth-weight infants have high levels of duodenal colonization with Enterobacteriaceae, with evidence of considerable cross-colonization with indistinguishable strains. There was no association between duodenal colonization with particular strains of Enterobacteriaceae and development of NEC.

Failure of systemic antibiotics to eradicate gram-negative bacilli from the airway of mechanically ventilated very low-birth-weight infants

BACKGROUND

Gram-negative bacillary (GNB) airway colonization in mechanically ventilated newborns is associated with morbidity and mortality, which may be reduced if systemic antimicrobial therapy eradicates GNB from the airway. Efforts to do so in adults have met with variable success; similar experiences in newborns have not been reported.

METHODS

From 1991 through 1998, 531 very low-birth-weight infants were mechanically ventilated longer than 2 weeks. The study group was 106 infants with GNB airway colonization. Sixty-four other neonates in whom GNB nosocomial bloodstream infections developed served as antibiotic treatment outcome control.

RESULTS

Isolated from the airway were enteric (70 cases) and environmental (36 cases) GNB. Gentamicin alone or with ceftazidime (79), ceftazidime (11), piperacillin in combination with tazobactam or tobramycin (8), and tobramycin, in combination with ampicillin/sulbactam or mezlocillin (8) were the antimicrobials selected. Systemic antibiotics failed to eradicate GNB colonization in 97% of the cases. Six of the 106 infants with airway colonization died for reasons unrelated to infection. Sixty-four infants experienced 67 bloodstream infections as a result of enteric (53) and environmental (14) GNB. Gentamicin alone (23), with ceftazidime (26), or with clindamycin or ampicillin/sulbactam (9), piperacillin with tazobactam or tobramycin (3) and ceftazidime alone (6) were the antimicrobials selected. Survival occurred in 84% of the 67 nosocomial bloodstream infections.

CONCLUSIONS

Systemic antibiotics do not consistently eradicate GNB from the airway of mechanically ventilated newborns, therefore its empirical use for prophylaxis or treatment of airway colonization should be discouraged.

Development of intestinal bacterial enzymes in infants--relationship to mode of delivery and type of feeding

To evaluate the development of intestinal flora in young infants, and especially to estimate the influence of mode of delivery and type of feeding on the establishment of intestinal microflora, faecal flora was studied indirectly by measuring prospectively the faecal bacterial enzyme activities (beta-glucosidase, beta-glucuronidase and urease) in 29 full-term, healthy infants during the first 6 months of life. Mode of delivery had no influence on the faecal enzyme activities. In contrast, infants receiving formula feeds were more often urease positive at 1-2 months of age (70% vs 25%, p=0.043) and had higher median activity of beta-glucuronidase at 6 months of age (0.90 and 0.19 nmoles/mg protein x min, p= 0.0043) than exclusively breast-fed infants. Through indirect methods to measure the development of a faecal microflora our results indicate that the type of milk that infants receive during the first months of life may have an important role in the development of intestinal flora.

Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery

BACKGROUND

Newborn infants in modern maternity hospitals are subject to numerous factors that affect normal intestinal colonization--for example, cesarean delivery and antimicrobial agents. To study the duration of the effect of external factors on intestinal colonization, two groups of infants with different delivery methods were investigated.

METHODS

The fecal flora of 64 healthy infants was studied prospectively. Thirty-four infants were delivered vaginally, and 30 by cesarean birth with antibiotic prophylaxis administered to their mothers before the delivery. The fecal flora was cultured on nonselective and selective media in infants 3 to 5, 10, 30, 60, and 180 days of age. Gastrointestinal signs were recorded daily by the mothers for 2 months.

RESULTS

The fecal colonization of infants born by cesarean delivery was delayed. Bifidobacterium-like bacteria and Lactobacillus-like bacteria colonization rates reached the rates of vaginally delivered infants at 1 month and 10 days, respectively. Infants born by cesarean delivery were significantly less often colonized with bacteria of the Bacteroides fragilis group than were vaginally delivered infants: At 6 months the rates were 36% and 76%, respectively (p=0.009). The occurrence of gastrointestinal signs did not differ between the study groups.

CONCLUSIONS

This study shows for the first time that the primary gut flora in infants born by cesarean delivery may be disturbed for up to 6 months after the birth. The clinical relevance of these changes is unknown, and even longer follow-up is needed to establish how long-lasting these alterations of the primary gut flora can be.

Nosocomial acquisition of Escherichia coli by infants delivered in hospitals

The delivery of infants in hospitals is desirable for obstetric reasons, but exposes the neonates to the microbiological hazards of a maternity unit. When neonates are born and cared for in hospital, the Escherichia coli strains that colonize the intestine tend to be acquired from the environment or from other babies, and are potentially pathogenic. The colonization of the infant with maternal flora should be promoted by strict rooming-in of mother and baby, or by delivery at home.